[BioC] array CGH

[Hilmar Berger]

Hi Lisa,

if after applying segmentation methods to your data the normal samples 
still indicate gains or losses you might want to have a look at 
http://projects.tcag.ca/variation/ for a list of known large scale copy 
number polymorphims.

Hilmar

Lisa Luo schrieb:
> Dear List,
> 
> I have a set of BAC array CGH data to analysis.  I am new to this kind of analysis.  Could anyone please recommend me a good package?
> 
> I read some papers on aCGH.  For the size of BAC clones, is averaging a few probes a good idea?  I tried DNAcopy and I am not happy with the results either.  Another question:  Can we use the ratio to call it amplification or deletion?  In my normal samples, I should expect ratio to be about 1.  But ratios in some probes/chromosomes tend to be high and ratios in another probes/regions tend to be lower.  So how to use the ratio?
> 
> Thank you so much for your help!
> 
> Lisa
> 
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-- 

Hilmar Berger
Studienkoordinator
Institut für medizinische Informatik, Statistik und Epidemiologie
Universität Leipzig
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D-04107 Leipzig

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email: hilmar.berger at imise.uni-leipzig.de